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musharna

plant-genomics-mcp

batch_get_gene_xrefs

Retrieve cross-references for up to 50 gene loci in parallel from Ensembl Plants, with per-locus results including count, xrefs, and database rollup.

Instructions

Batch variant of get_gene_xrefs. Fans out per-locus xref lookups over Ensembl Plants in parallel (up to 50 loci). Each results[locus] is the full single-locus shape (count + xrefs[] + by_db rollup).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
lociYesList of locus identifiers (1–50). Successes land in results[locus]; PlantGenomicsError failures in errors[locus].
organismNoPlant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxidarabidopsis_thaliana

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
toolYesThe batch tool name, e.g. batch_resolve_locus_to_uniprot
countYesNumber of loci in the input list
resultsYeslocus → per-locus result dict (same shape as the single-locus tool)
errorsYeslocus → '[ClassName] message' for PlantGenomicsError failures
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the burden. It discloses parallel fan-out, a 50-locus limit, and the result shape per locus. However, it omits mention of error behavior (though schema hints at errors[locus]) and rate limits.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two sentences, front-loaded with purpose and parallel behavior. Every sentence is informative and no redundant words.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the presence of an output schema, the description need not detail return values, but it helpfully outlines the result shape. It lacks mention of error handling (failures in errors[locus]), but overall it's complete for a batch query tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, but description adds value for 'loci' by explaining it triggers per-locus lookups with a concurrency limit. For 'organism', the schema already describes types and default, so no additional description is needed.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states 'Batch variant of get_gene_xrefs' and specifies it fans out per-locus xref lookups over Ensembl Plants in parallel. This distinguishes it from the single-locus sibling 'get_gene_xrefs' and other batch tools.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage when handling multiple loci (up to 50) by stating 'Fans out ... in parallel'. However, it lacks explicit when-not-to-use or alternative suggestions, though the sibling list includes the single-locus version.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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